Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6V4X

Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 Angstrom resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000243	cellular_component	commitment complex
A	0000387	biological_process	spliceosomal snRNP assembly
A	0000398	biological_process	mRNA splicing, via spliceosome
A	0003723	molecular_function	RNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005681	cellular_component	spliceosomal complex
A	0005682	cellular_component	U5 snRNP
A	0005683	cellular_component	U7 snRNP
A	0005684	cellular_component	U2-type spliceosomal complex
A	0005685	cellular_component	U1 snRNP
A	0005686	cellular_component	U2 snRNP
A	0005687	cellular_component	U4 snRNP
A	0005689	cellular_component	U12-type spliceosomal complex
A	0005697	cellular_component	telomerase holoenzyme complex
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006396	biological_process	RNA processing
A	0006397	biological_process	mRNA processing
A	0006479	biological_process	protein methylation
A	0008380	biological_process	RNA splicing
A	0016604	cellular_component	nuclear body
A	0019899	molecular_function	enzyme binding
A	0030532	cellular_component	small nuclear ribonucleoprotein complex
A	0034709	cellular_component	methylosome
A	0034715	cellular_component	pICln-Sm protein complex
A	0034719	cellular_component	SMN-Sm protein complex
A	0036261	biological_process	7-methylguanosine cap hypermethylation
A	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
A	0070034	molecular_function	telomerase RNA binding
A	0071005	cellular_component	U2-type precatalytic spliceosome
A	0071007	cellular_component	U2-type catalytic step 2 spliceosome
A	0071011	cellular_component	precatalytic spliceosome
A	0071013	cellular_component	catalytic step 2 spliceosome
A	0071208	molecular_function	histone pre-mRNA DCP binding
A	0071209	molecular_function	U7 snRNA binding
A	0097526	cellular_component	spliceosomal tri-snRNP complex
A	1903241	biological_process	U2-type prespliceosome assembly
A	1990904	cellular_component	ribonucleoprotein complex
B	0003723	molecular_function	RNA binding
C	0003723	molecular_function	RNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005683	cellular_component	U7 snRNP
C	0006397	biological_process	mRNA processing
C	0006398	biological_process	mRNA 3'-end processing by stem-loop binding and cleavage
C	0008380	biological_process	RNA splicing
C	0015030	cellular_component	Cajal body
C	0016604	cellular_component	nuclear body
C	0071208	molecular_function	histone pre-mRNA DCP binding
C	0071209	molecular_function	U7 snRNA binding
C	0071254	cellular_component	cytoplasmic U snRNP body
C	1900087	biological_process	positive regulation of G1/S transition of mitotic cell cycle
C	1990904	cellular_component	ribonucleoprotein complex
D	0003723	molecular_function	RNA binding
D	0071209	molecular_function	U7 snRNA binding
E	0000245	biological_process	spliceosomal complex assembly
E	0000387	biological_process	spliceosomal snRNP assembly
E	0000398	biological_process	mRNA splicing, via spliceosome
E	0003723	molecular_function	RNA binding
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005681	cellular_component	spliceosomal complex
E	0005682	cellular_component	U5 snRNP
E	0005683	cellular_component	U7 snRNP
E	0005684	cellular_component	U2-type spliceosomal complex
E	0005685	cellular_component	U1 snRNP
E	0005686	cellular_component	U2 snRNP
E	0005687	cellular_component	U4 snRNP
E	0005689	cellular_component	U12-type spliceosomal complex
E	0005697	cellular_component	telomerase holoenzyme complex
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006397	biological_process	mRNA processing
E	0008380	biological_process	RNA splicing
E	0030532	cellular_component	small nuclear ribonucleoprotein complex
E	0034709	cellular_component	methylosome
E	0034715	cellular_component	pICln-Sm protein complex
E	0034719	cellular_component	SMN-Sm protein complex
E	0036261	biological_process	7-methylguanosine cap hypermethylation
E	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
E	0071005	cellular_component	U2-type precatalytic spliceosome
E	0071007	cellular_component	U2-type catalytic step 2 spliceosome
E	0071011	cellular_component	precatalytic spliceosome
E	0071013	cellular_component	catalytic step 2 spliceosome
E	1903241	biological_process	U2-type prespliceosome assembly
E	1990904	cellular_component	ribonucleoprotein complex
F	0000387	biological_process	spliceosomal snRNP assembly
F	0000398	biological_process	mRNA splicing, via spliceosome
F	0003723	molecular_function	RNA binding
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005681	cellular_component	spliceosomal complex
F	0005682	cellular_component	U5 snRNP
F	0005683	cellular_component	U7 snRNP
F	0005684	cellular_component	U2-type spliceosomal complex
F	0005685	cellular_component	U1 snRNP
F	0005686	cellular_component	U2 snRNP
F	0005687	cellular_component	U4 snRNP
F	0005689	cellular_component	U12-type spliceosomal complex
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006397	biological_process	mRNA processing
F	0008380	biological_process	RNA splicing
F	0022618	biological_process	protein-RNA complex assembly
F	0030532	cellular_component	small nuclear ribonucleoprotein complex
F	0034709	cellular_component	methylosome
F	0034715	cellular_component	pICln-Sm protein complex
F	0034719	cellular_component	SMN-Sm protein complex
F	0036261	biological_process	7-methylguanosine cap hypermethylation
F	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
F	0071005	cellular_component	U2-type precatalytic spliceosome
F	0071007	cellular_component	U2-type catalytic step 2 spliceosome
F	0071013	cellular_component	catalytic step 2 spliceosome
F	1903241	biological_process	U2-type prespliceosome assembly
F	1990904	cellular_component	ribonucleoprotein complex
G	0000245	biological_process	spliceosomal complex assembly
G	0000387	biological_process	spliceosomal snRNP assembly
G	0000398	biological_process	mRNA splicing, via spliceosome
G	0003723	molecular_function	RNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005681	cellular_component	spliceosomal complex
G	0005682	cellular_component	U5 snRNP
G	0005683	cellular_component	U7 snRNP
G	0005684	cellular_component	U2-type spliceosomal complex
G	0005685	cellular_component	U1 snRNP
G	0005686	cellular_component	U2 snRNP
G	0005687	cellular_component	U4 snRNP
G	0005689	cellular_component	U12-type spliceosomal complex
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0006397	biological_process	mRNA processing
G	0008380	biological_process	RNA splicing
G	0030532	cellular_component	small nuclear ribonucleoprotein complex
G	0034709	cellular_component	methylosome
G	0034719	cellular_component	SMN-Sm protein complex
G	0036261	biological_process	7-methylguanosine cap hypermethylation
G	0043186	cellular_component	P granule
G	0046540	cellular_component	U4/U6 x U5 tri-snRNP complex
G	0071004	cellular_component	U2-type prespliceosome
G	0071005	cellular_component	U2-type precatalytic spliceosome
G	0071007	cellular_component	U2-type catalytic step 2 spliceosome
G	0071011	cellular_component	precatalytic spliceosome
G	0071013	cellular_component	catalytic step 2 spliceosome
G	0097526	cellular_component	spliceosomal tri-snRNP complex
G	1903241	biological_process	U2-type prespliceosome assembly
G	1990904	cellular_component	ribonucleoprotein complex
H	0003723	molecular_function	RNA binding
H	0004518	molecular_function	nuclease activity
H	0004519	molecular_function	endonuclease activity
H	0004521	molecular_function	RNA endonuclease activity
H	0004534	molecular_function	5'-3' RNA exonuclease activity
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005847	cellular_component	mRNA cleavage and polyadenylation specificity factor complex
H	0006397	biological_process	mRNA processing
H	0006398	biological_process	mRNA 3'-end processing by stem-loop binding and cleavage
H	0016787	molecular_function	hydrolase activity
H	0031124	biological_process	mRNA 3'-end processing
H	0046872	molecular_function	metal ion binding
H	0180010	biological_process	co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway
H	1900087	biological_process	positive regulation of G1/S transition of mitotic cell cycle
H	1990904	cellular_component	ribonucleoprotein complex
I	0003723	molecular_function	RNA binding
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005847	cellular_component	mRNA cleavage and polyadenylation specificity factor complex
I	0006397	biological_process	mRNA processing
I	0006398	biological_process	mRNA 3'-end processing by stem-loop binding and cleavage
I	0016020	cellular_component	membrane
I	0098794	cellular_component	postsynapse
I	0098978	cellular_component	glutamatergic synapse

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue ZN H 701

Chain	Residue
H	HIS71
H	HIS73
H	HIS158
H	ASP179
H	ZN702
Y	C27

site_id	AC2
Number of Residues	6
Details	binding site for residue ZN H 702

Chain	Residue
H	HIS418
H	ZN701
Y	C27
H	ASP75
H	HIS76
H	ASP179

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:19690332, ECO:0007744\|PubMed:24275569

Chain	Residue	Details
J	SER494
I	SER420

site_id	SWS_FT_FI2
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744\|PubMed:25114211, ECO:0007744\|PubMed:25218447, ECO:0007744\|PubMed:25755297, ECO:0007744\|PubMed:28112733

Chain	Residue	Details
J	LYS361
H	HIS73
H	ASP75
H	HIS76
H	HIS158
H	ASP179
H	HIS418

site_id	SWS_FT_FI3
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744\|PubMed:25218447, ECO:0007744\|PubMed:25755297, ECO:0007744\|PubMed:28112733

Chain	Residue	Details
I	SER660
J	LYS483

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:Q9QXK7

Chain	Residue	Details
H	SER659

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
H	THR681

site_id	SWS_FT_FI6
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) => ECO:0000269\|PubMed:17923699

Chain	Residue	Details
H	LYS462
H	LYS465
H	LYS545

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)